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PubMed2006

Isolation and quantification of oligomeric pyranoanthocyanin-flavanol pigments from red wines by combination of column chromatographic techniques.

A combination of column chromatography on Toyopearl gel HW-40 (S) and polyamide resin has been developed for the preparative isolation and further determination of pyranoanthocyanins of oligomeric nature formed after reaction between anthocyanins and different flavanols in a complex wine matrix. Polyamide chromatography was found to be exceptionally useful to separate oligomeric pyanoanthocyanins from other classes of wine flavonoids and polymerized pigments into an advanced state of purity for further identification and quantification by HPLC-diode array detector coupled with electrospray ionization mass spectrometry (HPLC-DAD/ESI-MS). Fractionation on Toyopearl gel chromatography allowed the separation of pyranoanthocyanins bearing the same flavanols (catechin, epicatechin and procyanidin dimers) but with different anthocyanin moieties (either acylated or non-acylated in the glucose residue) in order to allow further isolation of individual oligomeric pigments on C18 chromatography. A quantitative procedure for analyzing the major pyranoanthocyanin-flavanol derivatives in different aged wines is proposed for the first time. Results obtained showed good reproducibility and recovery regarding sample pretreatment and quantitative method for all analyzed oligomeric pyranoanthocyanins. The combination of these two chromatographic separations is likely to be applicable to the preparative isolation of other anthocyanin-derived pigments.

Chromatography, High Pressure Liquid↗
PubMed2007

Retention behavior of oligomeric proanthocyanidins in hydrophilic interaction chromatography.

A novel method was developed for the separation of proanthocyanidins (PAs; oligomeric flavan-3-ols) by hydrophilic interaction chromatography (HILIC) using an amide-silica column eluting with an aqueous acetonitrile mobile phase. The best separation was achieved with a linear gradient elution of acetonitrile-water at ratios of 9:1 to 5:5 (v/v) for 60 min at a flow rate of 1.0 ml/min. Under these HPLC conditions, a mixture of natural oligomeric PAs (from apple) was separated according to degree of polymerization (DP) up to decamers. The DP of each separated oligomer was confirmed by LC/electrospray ionization MS. In further HILIC separation studies of 15 different flavan-3-ol and oligomeric PA (up to pentamer) standards with an isocratic elution of acetonitrile-water (84:16), a high correlation was observed between the logarithm of retention factors (log k) and the number of hydroxyl groups in their structures. The coefficient of this correlation (r2=0.9501) was larger than the coefficient (r2=0.7949) obtained from the correlation between log k and log P(o/w) values. These data reveal that two effects, i.e. hydrogen bonding between the carbamoyl terminal on the column and the hydroxyl group of solute oligomer and hydrophilicity based on the high-order structure of oligomeric PAs, corporately contribute to the separation, but the hydrogen bonding effect is predominant in our HILIC separation mode.

Chromatography, High Pressure Liquid↗
PubMed2004

Volatile anesthetic modulation of oligomerization equilibria in a hexameric model peptide.

To determine if occupancy of interfacial pockets in oligomeric proteins by volatile anesthetic molecules can allosterically regulate oligomerization equilibria, variants of a three-helix bundle peptide able to form higher oligomers were studied with analytical ultracentrifugation, hydrogen exchange and modeling. Halothane shifted the oligomerization equilibria towards the oligomer only in a mutation predicted to create sufficient volume in the hexameric pocket. Other mutations at this residue, predicted to create a too small or too polar pocket, were unaffected by halothane. Inhaled anesthetic modulation of oligomerization interactions is a novel and potentially generalizable biophysical basis for some anesthetic actions.

Allosteric Regulation↗
PubMed2005

Solution structure of the symmetric coiled coil tetramer formed by the oligomerization domain of hnRNP C: implications for biological function.

During active cell division, heterogeneous nuclear ribonucleoprotein (hnRNP) C is one of the most abundant proteins in the nucleus. hnRNP C exists as a stable tetramer that binds about 230 nucleotides of pre-mRNA and functions in vivo to package nascent transcripts and nucleate assembly of the 40 S hnRNP complex. Previous studies have shown that monomers lacking or possessing mutant oligomerization domains bind RNA with low affinity, strongly suggesting a cooperative protomer-RNA binding mode. In order to understand the role of the oligomerization domain in defining the biological functions and structure of hnRNP C tetramers, we have determined the high-resolution NMR structure of the oligomerization interface that is formed at the core of the complex, examining specific molecular interactions that drive assembly and contribute to the structural integrity of the tetramer. The determined structure reveals an antiparallel four-helix coiled coil, where classically described knobs-into-holes packing interactions at interhelical contact surfaces are optimized so that side-chains interdigitate to create an even distribution of hydrophobic surfaces along the core. While the stoichiometry of the complex appears to be primarily specified by occlusion of hydrophobic surfaces, particularly the interfacial residue L198, from solvent, helix orientation is primarily determined by electrostatic attractions across helix interfaces. The creation of potential interaction surfaces for other hnRNP C domains along the coiled coil exterior and the assembly of oligomerization interfaces in an antiparallel orientation shape the tertiary fold of full-length monomers and juxtapose RNA-binding elements at distal surfaces of the tetrameric complex in the quaternary assembly. In addition, we discuss the specific challenges encountered in structure determination of this symmetric oligomer by NMR methods, specifically in sorting ambiguous interatomic distance constraints into classes that define different elements of the coiled coil structure.

Amino Acid Sequence↗
PubMed2006

Janus model of the Na,K-ATPase beta-subunit transmembrane domain: distinct faces mediate alpha/beta assembly and beta-beta homo-oligomerization.

Na,K-ATPase is a hetero-oligomer of alpha and beta-subunits. The Na,K-ATPase beta-subunit (Na,K-beta) is involved in both the regulation of ion transport activity, and in cell-cell adhesion. By structure prediction and evolutionary analysis, we identified two distinct faces on the Na,K-beta transmembrane domain (TMD) that could mediate protein-protein interactions: a glycine zipper motif and a conserved heptad repeat. Here, we show that the heptad repeat face is involved in the hetero-oligomeric interaction of Na,K-beta with Na,K-alpha, and the glycine zipper face is involved in the homo-oligomerization of Na,K-beta. Point mutations in the heptad repeat motif reduced Na,K-beta binding to Na,K-alpha, and Na,K-ATPase activity. Na,K-beta TMD homo-oligomerized in biological membranes, and mutation of the glycine zipper motif affected oligomerization and cell-cell adhesion. These results provide a structural basis for understanding how Na,K-beta links ion transport and cell-cell adhesion.

Amino Acid Sequence↗
PubMed2004

KSHV LANA1 binds DNA as an oligomer and residues N-terminal to the oligomerization domain are essential for DNA binding, replication, and episome persistence.

Latency-associated nuclear antigen 1 (LANA1) binds to Kaposi's sarcoma-associated herpesvirus (KSHV) terminal repeat (TR) DNA to mediate episome replication and persistence. LANA1 concentrates at sites of TR DNA along mitotic chromosomes, consistent with tethering KSHV DNA to chromosomes for efficient segregation of episomes to progeny nuclei. We now investigate LANA1 C-terminus self-association and DNA binding. The TR DNA binding domain was localized to LANA1 residues 996-1139. Scanning deletions within this region ablated both LANA1 oligomerization and DNA binding, consistent with a requirement for oligomerization to bind DNA. Furthermore, LANA1 bound TR DNA as an oligomer. Deletion of amino acids 1007-1021, N-terminal to the LANA1 oligomerization domain, ablated DNA binding, DNA replication, and episome persistence, implicating these residues in contacting DNA. Indeed, LANA1 residues 1007-1021 correspond to EBNA1 residues that contact the cognate sequence. Like EBNA1, the LANA1 DNA-binding domain has oligomerization activity and critical residues essential for recognizing DNA.

Animals↗
PubMed2002

Dimeric and oligomeric surfactants. Behavior at interfaces and in aqueous solution: a review.

Dimeric and oligomeric surfactants are novel surfactants that are presently attracting considerable interest in the academic and industrial communities working on surfactants. This paper first presents a number of chemical structures that have been reported for ionic, amphoteric and nonionic dimeric and oligomeric surfactants. The following aspects of these surfactants are then successively reviewed the state of dimeric and oligomeric surfactants in aqueous solutions at concentration below the critical micellization concentration (cmc); their behavior at the air/solution and solid/solution interfaces; their solubility in water, cmc and thermodynamics of micellization; the properties of the aqueous micelles of dimeric and oligomeric surfactants (ionization degree, size, shape, micropolarity and microviscosity, solution microstructure, solution rheology, micelle dynamics, micellar solubilization, interaction between dimeric surfactants and water-soluble polymers); the mixed micellization of dimeric surfactants with various conventional surfactants; the phase behavior of dimeric surfactants and the applications of these novel surfactants.

Journal Article↗
PubMed2002

Preformed oligomeric epidermal growth factor receptors undergo an ectodomain structure change during signaling.

Fluorescence resonance energy transfer (FRET) was used to reveal aspects of the mechanism of signal transduction by epidermal growth factor receptors (EGFR). The superpositions of epidermal growth factor (EGF), transforming growth factor-alpha (TGFalpha) and an antibody fragment (29.1) to the carbohydrate extremity of the receptor's ectodomain as measured by FRET, show that 14% of EGFRs in A431 cells are oligomerized before growth factor binding. After binding growth factor and signaling, these oligomers dissociate before releasing growth factor. Time courses of the FRET-derived distances between constitutively oligomerized EGFRs during signal transduction show a transient structural change in the extracellular domain, which occurs simultaneously with the production of intracellular Ca2+ signals. The FRET measurements also show a slow increase in oligomerization of EGFR monomers after growth factor binding. The structural change found in the extracellular domain of oligomeric EGFRs is similar to that shown by others for EPO, Neu, Fas, and tumor necrosis factor receptors, and may therefore be a common property of the transduction of the receptor-mediated signals.

Calcium Signaling↗
PubMed2003

Simulations of oligomeric intermediates in prion diseases.

We extend our previous stochastic cellular automata-based model for two-dimensional (areal) aggregation of prion proteins on neuronal surfaces. The new anisotropic model allows us to simulate both strong beta-sheet and weaker attachment bonds between proteins. Constraining binding directions allows us to generate aggregate structures with the hexagonal lattice symmetry found in recently observed in vitro experiments. We argue that these constraints on rules may correspond to underlying steric constraints on the aggregation process. We find that monomer-dominated growth of the areal aggregate is too slow to account for some observed doubling-time-to-incubation-time ratios inferred from data, and so consider aggregation dominated by relatively stable but noninfectious oligomeric intermediates. We compare a kinetic theory analysis of oligomeric aggregation to spatially explicit simulations of the process. We find that with suitable rules for misfolding of oligomers, possibly due to water exclusion by the surrounding aggregate, the resulting oligomeric aggregation model maps onto our previous monomer aggregation model. Therefore it can produce some of the same attractive features for the description of prion incubation time data. We propose experiments to test the oligomeric aggregation model.

Algorithms↗
PubMed1998

Oligomeric state of human erythrocyte band 3 measured by fluorescence resonance energy homotransfer.

The oligomeric state of the erythrocyte anion exchange protein, band 3, has been assayed by resonance energy homotransfer. Homotransfer between oligomeric subunits, labeled with eosin-5-maleimide at Lys430 in the transmembrane domain, has been demonstrated by steady-state and time-resolved fluorescence spectroscopy, and is readily observed by its depolarization of the eosin fluorescence. Polarized fluorescence measurements of HPLC-purified band 3 oligomers indicate that eosin homotransfer increases progressively with increasing species size. This shows that homotransfer also occurs between labeled band 3 dimers as well as within the dimers, making fluorescence anisotropy measurements sensitive to band 3 self-association. Treatment of ghost membranes with either Zn2+ or melittin, agents that cluster band 3, significantly decreases the anisotropy as a result of the increased homotransfer within the band 3 clusters. By comparison with the anisotropy of species of known oligomeric state, the anisotropy of erythrocyte ghost membranes at 37 degrees C is consistent with dimeric and/or tetrameric band 3, and does not require postulation of a fraction of large clusters. Proteolytic removal of the cytoplasmic domain of band 3, which significantly increases the rotational mobility of the transmembrane domain, does not affect its oligomeric state, as reported by eosin homotransfer. These results support a model in which interaction with the membrane skeleton restricts the mobility of band 3 without significantly altering its self-association state.

Anion Exchange Protein 1, Erythrocyte↗
PubMed2000

Regulated but not constitutive human respiratory syncytial virus (HRSV) P protein phosphorylation is essential for oligomerization.

Purified human respiratory syncytial virus (HRSV) P phosphoprotein from transfected HEp-2 cells is able to oligomerize forming tetramers. The bulk of constitutive P protein phosphorylation (99. 8%) (serine residues 116, 117, 119, 232 and 237) can be removed without affecting protein oligomerization. However, dephosphorylated P protein, produced in bacteria, is unable to oligomerize. This difference can be explained by a transient P protein phosphorylation, detected in HEp-2 cells, that could be essential for P protein oligomerization.

Amino Acid Sequence↗
PubMed1998

Cross-linking and mutational analysis of the oligomerization state of the cytokine macrophage migration inhibitory factor (MIF).

The structure of the cytokine MIF has been investigated by X-ray crystallography, NMR, and biochemical methods with conflicting results regarding the structural and functional oligomerization state of this protein. Determination of the oligomeric state(s) is important for understanding more precisely the molecular mechanism of MIF action. To address this issue, we performed cross-linking of human and mouse MIF and selected mutants by various methods and analyzed the oligomerization by SDS-PAGE and gel filtration. MIF was found to form a mixture of monomeric, dimeric, and trimeric states at physiological concentrations, with the monomer and dimer representing the major species. Similar results were obtained when the carboxy-truncated mutants MIF(1-104) and MIF(1-109) were examined, indicating that the C-terminus of MIF is not critical for trimer stabilization. Cross-linking analysis of the isosteric Cys --> Ser mutants C56S and C80S of human MIF resulted in a similar oligomer distribution, whereas substitution of Cys59 led to a significant reduction in the dimeric and trimeric forms, indicating that the hydrophobic region around Cys59 is important for the oligomerization of MIF. Together, our data argue that physiological MIF solutions contain a mixture of monomers, dimers, and trimers.

Animals↗
PubMed2002

Multiple oligomeric states of the Helicobacter pylori vacuolating toxin demonstrated by cryo-electron microscopy.

Helicobacter pylori vacuolating toxin (VacA) is a bacterial protein toxin that forms water-soluble oligomeric complexes, and can somehow insert into lipid bilayers to produce anion-selective channels. In this study, we utilize the novel technique of "cryo-negative staining" to examine the morphology of vitrified VacA complexes. Two basic types of oligomeric structures were observed: (i) relatively thick six or seven-sided astral arrays with near-perfect radial symmetry; and (ii) relatively thin astral arrays of six to nine short "rodlets" that display a distinct handedness or "chirality". Additionally, the new technique provided edge-views of the thicker form of VacA oligomer, which appears to be a thin bilayered disc, indicating that the relatively thick six-sided arrays are actually dodecamers. Also observed occasionally in the present cryo-negatively stained VacA preparations were 2D crystalline arrays that appeared to be comprised of interlocked dodecamers. The structural alterations that VacA oligomers must undergo to form these 2D crystals were analyzed, and intermediates in this transition were identified. Additionally, the oligomeric state of acid-activated VacA bound to membranes was visualized by the traditional technique of "deep-etch" electron microscopy, and was found to resemble most closely the top halves of the dodecamers. These results indicate that VacA is able to undergo major conformational changes, accompanied by major changes in its state of oligomerization, under different natural and experimental conditions.

Animals↗
PubMed2002

Influence of oligomeric silicic and humic acids on aluminum accumulation in a freshwater grazing invertebrate.

This study examined the influence of oligomeric silicic acid and humic acid on aluminum in the water column and its accumulation in the freshwater snail Lymnaea stagnalis. Forty-eight hours after addition of Al (500 microg L(-1)), 83% of the metal was lost from the water column. This loss was reduced by oligomeric silica (20 mg L(-1)) and by humic acid (10 mg L(-1)). Aluminum accumulated in the digestive gland and, to a lesser extent, in the remaining soft tissues, and this accumulation was reduced by oligomeric silica. In the presence of humic acid, Al accumulation in the digestive gland was unaffected, though less was accumulated in the remaining tissues. Snails accumulated Si preferentially in the digestive gland and this accumulation was increased in the presence of added Al. Thus, both oligomeric silica and humic acid influence Al bioavailability and Si is upregulated in the digestive gland in the presence of Al.

Aluminum↗
PubMed2003

Dopamine receptor hetero-oligomerization: a hypothesis for behavioral sensitization to psychostimulants.

Repeated psychostimulant pretreatment can induce behavioral sensitization. Many previous studies have demonstrated that receptors of the dopamine and other neurotransmitter systems are involved in the sensitization process, however, the precise mechanism of this interaction is still unknown. We propose the hypothesis that oligomerization of the dopamine receptors and analogs from other neurotransmitter systems may contribute, at least in part, to psychostimulant-induced behavioral sensitization. Psychostimulant exposure can enhance central dopamine release, which can increase oligomerization of the dopamine receptors with their analogs. Receptor oligomerization can enhance the functional properties of the receptors and affect receptor degradation, which may be related to the behavioral augmentation which characterizes the sensitized state and produces the persistence of behavioral sensitization. The proposed receptor hetero-oligomerization model may provide a new direction in the exploration of the functionally critical sensitization phenomenon.

Amphetamines↗
PubMed1997

Alpha-helical coiled-coil oligomerization domains in extracellular proteins.

Subunit oligomerization of many proteins is mediated by alpha-helical coiled-coil domains. 3,4-Hydrophobic heptad repeat sequences, the characteristic feature of the coiled-coil protein folding motif, have been found in a wide variety of gene products including cytoskeletal, nuclear, muscle, cell surface, extracellular, plasma, bacterial, and viral proteins. Whereas the majority of coiled-coil structures is represented by intracellular alpha-helical bundles that contain two polypeptide chains, examples of extracellular coiled-coil proteins are fewer in number. Most proteins located in the extracellular space form three-stranded alpha-helical assemblies. Recently, five-stranded coiled coils have been identified in thrombospondins 3 and 4 and in cartilage oligomeric matrix protein, and the formation of a heterotetramer has been observed in in vitro studies with the recombinant asialoglycoprotein receptor oligomerization domain. Coiled-coil domains in laminins and probably also in tenascins and thrombospondins are responsible for the formation of tissue-specific isoforms by selective oligomerization of different polypeptide chains.

Amino Acid Sequence↗
PubMed1999

Genetic selection of short peptides that support protein oligomerization in vivo.

An important goal in protein engineering is to control associations between designed proteins. This is most often done by fusing known, naturally occurring oligomerization modules, such as leucine zippers [1] [2] [3], to the proteins of interest [4] [5] [6]. It is of considerable interest to design or discover new oligomerization domains that have novel binding specificities [7] [8] [9] [10] [11] in order to expand the 'toolbox' of the protein engineer and also to eliminate associations of the designed proteins with endogenous factors. We report here a simple genetic selection scheme through which to search libraries for peptides that are able to mediate homodimerization or higher-order self-oligomerization of a protein in vivo. We found several peptides that support oligomerization of the lambda repressor DNA-binding domain in Escherichia coli cells, some of them as efficiently as the endogenous dimerization domain or the GCN4 leucine zipper. Many are very small, comprising as few as six residues. This study strongly supports the notion that peptide sequence space is rich in small peptides, which might be useful in protein engineering and other applications.

Amino Acid Sequence↗
PubMed1997

Proline-dependent oligomerization with arm exchange.

BACKGROUND: Oligomerization is often necessary for protein activity or regulation and its efficiency is fundamental for the cell. The quaternary structure of a large number of oligomers consists of protomers tightly anchored to each other by exchanged arms or swapped domains. However, nothing is known about how the arms can be kept in a favourable conformation before such an oligomerization. RESULTS: Upon examination of such quaternary structures, we observe an extremely frequent occurrence of proline residues at the point where the arm leaves the protomer. Sequence alignment and site-directed mutagenesis confirm the importance of these prolines. The conservation of these residues at the hinge regions can be explained by the constraints that they impose on polypeptide conformation and dynamics: by rigidifying the mainchain, prolines favour extended conformations of arms thus favouring oligomerization, and may prevent interaction of the arms with the core of the protomer. CONCLUSIONS: Hinge prolines can be considered as 'quaternary structure helpers'. The presence of a proline should be considered when searching for a determinant of oligomerization with arm exchange and could be used to engineer synthetic oligomers or to displace a monomers to oligomers equilibrium by mutation of this proline residue.

Acetyltransferases↗